The France international was on the scoresheet in the 10th minute of the European clash, but he was forced off the field before the interval due to a muscular problem.
After the match, Los Blancos head coach Carlo Ancelotti said that Mbappe was only suffering with "an overload", suggesting that he would be available for Saturday's La Liga clash against Rayo Vallecano.
However, Real Madrid have now confirmed a thigh problem for the ex-Monaco youngster, which will sideline him for at least this weekend's league fixture with Rayo Vallecano and also likely the final of the Intercontinental Cup.
"Following the tests carried out today on our player Kylian Mbappe by the Real Madrid Medical Services, he has been diagnosed with an injury to the thigh of his left leg. Pending evolution," read a statement from the Spanish and European champions.
Mbappe 'set' to miss Real Madrid's 'next two matches'
Los Blancos have not provided a timeframe when it comes to the attacker's recovery, but according to journalist Alberto Pereiro, Mbappe is expected to be sidelined for the next 10 days.
If that is the case, the Frenchman would miss Saturday's La Liga game against Rayo Vallecano in addition to the final of the Intercontinental Cup on December 18, which will be against either Pachuca or Al Ahly.
Pereiro claims that Mbappe may still make the trip to Qatar, but it is unlikely that he will play, with his return expected to come against Sevilla on December 22 in what will be the team's final game ahead of the winter break.
Mbappe has faced criticism for his performances since arriving at Real Madrid, but the 25-year-old has still come up with 12 goals and two assists in 22 appearances in all competitions for Ancelotti's side.
Which other players are currently injured for Real Madrid?
There had also been concern surrounding Jude Bellingham's fitness after the clash with Atalanta, but the England international is expected to be available for the clash against Rayo Vallecano.
Eduardo Camavinga is also in the latter stages of his recovery from a hamstring issue and could travel with the team to Qatar, while Ferland Mendy may also be back before the end of the year, as his muscular problem is not serious.
Eder Militao and Dani Carvajal are both out for the season with serious knee injuries, but David Alaba's return after more than one year on the sidelines with an ACL issue of his own will come in January.
Real Madrid would move to the top of the La Liga table if they triumph on Saturday, and the capital outfit will be bidding to make it three straight victories in all competitions when they face Los Franjirrojos at Campo de Futbol de Vallecas.
Written by
Matt Law